Abstract 3381: Analytical performance of an ultra-sensitive, tumor-informed liquid biopsy platform for molecular residual disease detection and clinical guidance
Authors: Rui Chen, Gábor Bartha, John Lyle, Jason Harris, Sean M. Boyle, Josette Northcott, Dan Norton, Rachel M. Pyke, Fábio C. Navarro, Charles W. Abbott, Christian Haudenschild, Rose Santiago, Darren Nichols, Stephanie Huang, Christopher Nelson, Manju Chinnappa, Yi Chen, Yuker Wang, Laurie Goodman, Qi Zhang, Manqing Hong, Xiaoji Chen, Erin Ayash, Nitin Udar, Sebastian Saldivar, Jian Yan, John West, Richard O. Chen
Journal: Cancer Research (2023)

Abstract Most circulating tumor DNA (ctDNA)-based molecular residual disease (MRD) detection methods leverage a limited genomic footprint, restricting detection sensitivity to 10-4 ~ 10-5 tumor fraction and thus their utility in many clinical settings. For example, early-stage, low tumor mutational burden (TMB) cancers may lack sufficient variants in these limited footprints to produce detectable signals. Further, insights into tumor evolution, including actionable mutations may be missed.Here we report a performance update of the NeXT Personal™️ platform. Utilizing whole genome sequencing of tumor and normal DNA to guide design of bespoke MRD assays, we select up to 1800 high signal, low noise MRD targets and up to 400 exonic variants. Along with proprietary algorithms, this achieves high sensitivity with a limit of detection of 1 ~ 3 parts per million, and targets high specificity (99.99%). Specificity was demonstrated with healthy donor plasma samples and &amp;gt; 200 cancer patient panels from a broad range of solid tumors. Sensitivity and linearity of MRD measurements were determined using dilution series from cell lines and clinical samples, which were orthogonally confirmed (R2 = 0.909, PPA = 100%, NPA = 100%) by digital droplet PCR (ddPCR).In addition, NeXT Personal simultaneously surveys tumor-agnostic content in the same workflow, providing detection of actionable mutations, markers of drug resistance, and mechanisms of tumor evolution from a curated set of variants in 90 clinically-relevant genes. Patient plasma (1 ~ 8 mL; 2 ~ 50 ng of cfDNA) can be rapidly queried to provide mutation-level information about tumor biology, longitudinal trajectory, and clinical actionability. The specificity of NeXT Personal variant detection is &amp;gt; 99.99% with 100% PPV, while individual variant content demonstrates high sensitivity at allele fractions of 0.1% and above, with high accuracy and signal linearity as confirmed by ddPCR (R2 = 0.998).To explore the utility of NeXT Personal in a clinical setting, a retrospective analysis was undertaken in an advanced liver cancer (low TMB) cohort of 11 patients undergoing immunotherapy. Our results demonstrated that changes in ctDNA levels during therapy correlated highly with disease status (6wk vs. baseline, p = 0.017; 9wk vs. baseline, p = 0.004), and were detected prior to clinical response confirmation by RECIST 1.1. Examination of the clinical content provided useful insights into the potential of the assay.Our data demonstrate high analytical performance of the NeXT Personal platform in both MRD and individual variant detection. The assay is sufficiently sensitive for early stage, low shedding, and low TMB cancers, early time points or samples with limited input. The addition of clinically relevant tumor-agnostic actionable content makes NeXT Personal unique in its ability to detect MRD and to ultimately help guide clinicians. Citation Format: Rui Chen, Gábor Bartha, John Lyle, Jason Harris, Sean M. Boyle, Josette Northcott, Dan Norton, Rachel M. Pyke, Fábio C. Navarro, Charles W. Abbott, Christian Haudenschild, Rose Santiago, Darren Nichols, Stephanie Huang, Christopher Nelson, Manju Chinnappa, Yi Chen, Yuker Wang, Laurie Goodman, Qi Zhang, Manqing Hong, Xiaoji Chen, Erin Ayash, Nitin Udar, Sebastian Saldivar, Jian Yan, John West, Richard O. Chen. Analytical performance of an ultra-sensitive, tumor-informed liquid biopsy platform for molecular residual disease detection and clinical guidance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3381.